I guess we all have gone through it. How to convert one "PDB format" into another "PDB format". You do CHARMM, you get some output, you want to do something else and you need to change to use it as an input to another program.
There can not be one converter/parser for all. Sometimes you need to convert CHARMM PDB files into ROSETTA-like. What to do?
For me it seems to be very useful to work with the library of functions, and then take what I need for a particular case as set of operations (like,
--rosetta2generic). This project at github is pretty new, although it used some functions for a few years now.
You can use the functions as library, you can use the program (just a simple example) to run it in the console:
$ ./yapdb_parser.py -h usage: yapdb_parser [-h] [-r] [-c] [--getchain GETCHAIN] [--getseq] [--rosetta2generic] [--getrnapuzzle] file positional arguments: file file optional arguments: -h, --help show this help message and exit -r, --report get report -c, --clean get clean structure --getchain GETCHAIN get chain, .e.g A --getseq get seq --rosetta2generic convert ROSETTA-like format to generic pdb --getrnapuzzle get RNApuzzle ready
Why I think it might be interesting for some of you:
- you see input & output files at github -- is this what you want to get?
- it's tested via Travis! -- it (should) always works as you just want!
- you miss a converter you would like to have? Just Do It Yourself - compose your converter/parser from LEGO brick-like functions, see
I share it with you, maybe someone will find it useful.
It would be fun if anyone could contribute with one functions. We will see how it goes.
It useful for me right now. I used the project as a parser for our new RNA-protein & DNA-protein docking method (http://iimcb.genesilico.pl/NPDock/ ).
Join the project, comment, clone, pull, enjoy! If you have any comments, then you are well welcome.
I hope someone will find it useful.